HCA Data Portal

Analysis process

Information about the analysis process.

View JSON source: analysis_processdoneShow required fields only


Analysis run typeRequiredanalysis_process.analysis_run_typecopy (string enum) Whether the analysis was run or was copied forward as an optimization. Should be one of: "run" or "copy-forward".
Reference filesRequiredanalysis_process.reference_filescopy (array) UUID of the file entities that contain the reference genome used in running the pipeline.
Start timestamp (UTC)Requiredanalysis_process.timestamp_start_utccopy (string) Initial start time of the full pipeline in UTC. For example "2018-01-21T09:34:27Z".
Stop timestamp (UTC)Requiredanalysis_process.timestamp_stop_utccopy (string) Terminal stop time of the full pipeline in UTC. For example "2018-01-21T11:35:01Z".
Analysis process>Input parametersRequired (analysis_process array) Input parameters used in the pipeline run.
Checksumanalysis_process.inputs.checksumcopy (string from analysis_process) MD5 checksum of the file. For example "e09a986c2e630130b1849d4bf9a94c06".
Parameter nameRequiredanalysis_process.inputs.parameter_namecopy (string from analysis_process) Name of parameter. For example "stranded" or "rsem_ref_index".
Parameter valueRequiredanalysis_process.inputs.parameter_valuecopy (string from analysis_process) Path to file for or value of parameter. For example "NONE" or "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode_v27_primary.tar".
Analysis process>Workflow tasksRequired (analysis_process array) Information about steps in the workflow.
CPUsRequiredanalysis_process.tasks.cpuscopy (integer from analysis_process) Number of CPUs used to run this task. For example "2".
Disk nameRequiredanalysis_process.tasks.disk_sizecopy (string from analysis_process) Name of the disk volume mounted to the VM for the task. For example "local-disk 11 HDD".
Docker imageRequiredanalysis_process.tasks.docker_imagecopy (string from analysis_process) Name of docker image where the task is stored and executed. For example "quay.io/humancellatlas/secondary-analysis-picard:v0.2.2-2.10.10".
Log erroranalysis_process.tasks.log_errcopy (string from analysis_process) Path where standard error is logged.
Log outanalysis_process.tasks.log_outcopy (string from analysis_process) Path where standard output is logged.
MemoryRequiredanalysis_process.tasks.memorycopy (string from analysis_process) Amount of memory allocated for this task. For example "7.5 GB".
Start timeRequiredanalysis_process.tasks.start_timecopy (string from analysis_process) Date and time when the task started. For example "2019-04-23T20:25:25.969Z".
Stop timeRequiredanalysis_process.tasks.stop_timecopy (string from analysis_process) Date and time when the task finished. For example "2019-04-23T20:28:29.830Z".
Task nameRequiredanalysis_process.tasks.task_namecopy (string from analysis_process) Name of the task. For example "CollectDuplicationMetrics" or "RSEMExpression".
ZoneRequiredanalysis_process.tasks.zonecopy (string from analysis_process) Name of the Google Cloud zone where the task was run. For example "us-central1-b" or "europe-north1-a".
Analysis process>Process typeRequired (process_type_ontology object) The type of process.
Process type ontology IDanalysis_process.type.ontologycopy (string from process_type_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0009128" or "EFO:0009121".Graph restriction: Subclasses of EFO:0002694 from obo:efo.
Process type ontology labelanalysis_process.type.ontology_labelcopy (string from process_type_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "enzymatic dissociation" or "blood draw".
Process typeRequiredanalysis_process.type.textcopy (string from process_type_ontology) The name of a process type being used. For example "enzymatic dissociation" or "blood draw".
Analysis process>Process coreRequired (process_core object) Core process-level information.
Locationanalysis_process.process_core.locationcopy (string from process_core) Location where the process took place. For example "Wellcome Trust Sanger Institute" or "Cancer Institute Stanford University".
Operator(s)analysis_process.process_core.operatorscopy (array from process_core) Identifier for individual(s) who executed the process. For example "Technician 1", "JD" or "John Doe".
Process descriptionanalysis_process.process_core.process_descriptioncopy (string from process_core) A general description of the process.
Process IDRequiredanalysis_process.process_core.process_idcopy (string from process_core) A unique ID for the process.
Process nameanalysis_process.process_core.process_namecopy (string from process_core) A short, descriptive name for the process that need not be unique.
Analysis process>provenance (provenance object) Provenance information provided by the system.
Accessionanalysis_process.provenance.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredanalysis_process.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versionanalysis_process.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versionanalysis_process.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredanalysis_process.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDanalysis_process.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update dateanalysis_process.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDanalysis_process.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.